WHO chief Tedros Adhanom Ghebreyesus said he had been subjected to racist comments and death threats for months.
But President Tsai Ing-wen said Taiwan opposed any form of discrimination, and invited Dr Tedros to visit the island.
Taiwan said it had been denied access to vital information as the coronavirus spread. The WHO rejects this.
The Chinese Communist Party regards Taiwan as a breakaway province and claims the right to take it by force if necessary.
What is being said?
Dr Tedros said he had been at the receiving end of racist comments for the past two to three months.
“Giving me names, black or negro,” he said. “I’m proud of being black, or proud of being negro.”
He then said he had received death threats, adding: “I don’t give a damn.”
The WHO chief said the abuse had originated from Taiwan, “and the foreign ministry didn’t disassociate” itself from it.
But Ms Tsai said Taiwan was opposed to discrimination.
“For years, we have been excluded from international organisations, and we know better than anyone else what it feels like to be discriminated against and isolated,” Reuters news agency quoted her as saying.
“If Director-General Tedros could withstand pressure from China and come to Taiwan to see Taiwan’s efforts to fight Covid-19 for himself, he would be able to see that the Taiwanese people are the true victims of unfair treatment.”
Taiwan foreign ministry spokeswoman Joanne Ou said the comments were “irresponsible” and the accusations “imaginary”. The ministry said it was seeking an apology for “slander”, AFP news agency reported.
Correspondents say Taiwan has been proud of its measures to contain the virus, with just 380 cases and five deaths so far.
Last month, the WHO said it was monitoring the progress of the virus in Taiwan and learning lessons from its efforts.